Re: Treatment of a Neutral N-terminus

From: Thomas Gaillard (gaillard_at_chimie.u-strasbg.fr)
Date: Fri Jul 20 2007 - 13:29:39 CDT

On Fri, Jul 20, 2007 at 05:51:32PM +0100, Maria Bagonis wrote :
> Dear all,
>
> In my current simulation it is necessary for me to treat the N-terminus of an
> amino acid as deprotonated/neutral. I was wondering if anyone had any
> suggestions about the best way to do such. I don't believe such a patch is
> included in the CHARMM file that I am using (The standard combined All-Hydrogen
> Topology File for CHARMM22 Proteins and CHARMM27 Lipids). I have found a patch
> in the AMINOH.RTF file (the topology file for CHARMM version 22 (All
> Hydrogens)). However, I am unsure if this is the best way to characterize the
> group, or if it is even valid to combine these two files.
> Any insight into the best way to proceed would be greatly appreciated. (I'm
> assuming this problem is likely encountered fairly frequently). Thanks!
>
> -Maria

Hello Maria,

You could use the neutral ACE patch (acetylated N-terminus) instead of
NTER when you generate your segment. This patch is indeed present in
top_all27_prot_lipid.rtf.

Regards,

-- 
Thomas Gaillard
Laboratoire de Biophysicochimie Moléculaire
Institut de Chimie LC3 - UMR 7177
Université Louis Pasteur
4 rue Blaise Pascal
F-67000 Strasbourg
phone: +33 (0)390 241 493
fax: +33 (0)390 241 490
mail: gaillard_at_chimie.u-strasbg.fr
web: http://lbm.u-strasbg.fr/gaillard

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:46:40 CST